Hi Chris,
Thank you again for your assistance and time.
I have installed JAVE SE update 38
By replacing in the script
"set JAVA_COMMAND=java"
by "set JAVA_COMMAND=C:\Program Files\Java\jre6\bin\java.exe"
makes the script not able to start, displaying:
"C:\Program is not recognized as an internal or external command operable
program or batch file. Press any key to continue....."
I uninstalled java 7, leaving only Java 6 and set "set JAVA_COMMAND=java"
But again i am experiencing the same issue as when I was using Java 7, the
program is crashing, especially when I am trying to save the project.
Is there anything else that I could try?
Thank you
Cheers
Kostas
-----Original Message-----
From: Pudney Chris (ext) GBJH [mailto:chris.pud...@syngenta.com]
Sent: December-19-12 1:30 AM
To: Konstantinos Aliferis, Dr
Cc: mzmine-devel@lists.sourceforge.net
Subject: Re: [Mzmine-devel] MZmine troubleshooting
G'day,
Kostas, the log file does indeed indicate that Java crashed during XCMS
deconvolution and that it occurred in JRI, the Java <-> R interface.
My only other suggestion is that you try the latest Java SE 6. You should be
able to install it alongside Java SE 7. In which case you will need to update
your start-up script by changing the following line:
set JAVA_COMMAND=java
to one that uses Java SE 6 explicitly. It will look something like:
set JAVA_COMMAND=C:\Program Files\Java\jre6\bin\java.exe
Regards,
Chris.
On 19/12/12 12:55, Konstantinos Aliferis, Dr wrote:
> Hi Chris,
> Thank you for your prompt reply and assistance.
>
> I have noticed that the error occurs during XCMS chromatogram deconvolution
> as well as during saving projects when XCMS mass lists are included.
> Omitting the XCMS mass lists no error occurs while saving projects.
>
> I have the JAVA(TM) Platform SE 7 U10 (v. 7.0.100.18) installed.
>
> Regarding the settings in the starting script, indeed it was the wrong path,
> now it is corrected.
> Please find attached the error log (it is the only one in the directory).
>
> Thank you
> Kostas
>
> -----Original Message-----
> From: Pudney Chris (ext) GBJH [mailto:chris.pud...@syngenta.com]
> Sent: December-18-12 10:05 PM
> To: Konstantinos Aliferis, Dr;
> mzmine-devel@lists.sourceforge.net<mailto:mzmine-devel@lists.sourceforge.net>
> Subject: Re: [Mzmine-devel] MZmine troubleshooting
>
> G'day,
>
> Glad you were able to get things working.
>
> You say that the XCMS module isn't working but the screenshot you attached
> shows that the task in progress is "Saving project", not XCMS deconvolution.
>
> When in your work flow is this error occurring?
>
> I think this particular error could be a problem with the Java SE run-time
> environment (JRE). This usually writes a hs_err_pidXXXXXX.log file in the
> directory of MZmine start up script. Next time the error occurs can you look
> for the (most recent) log file and send it to the list please?
>
> Which version of Java are you running? The following command will tell you:
>
> java -version
>
> If it's not the latest version then download the latest JRE (Java SE 6 or 7)
> for Windows 64-bit:
> http://www.oracle.com/technetwork/java/javase/downloads/index.html
>
> Finally, I noticed in your MZmine start-up script the following line:
>
> set JRI_LIB_PATH=C:\Users\KAA
> FLB\Documents\R\win-library\2.15\rJava\jri\i386
>
> I believe you're running 64-bit Windows so I think this line should be
>
> set JRI_LIB_PATH=C:\Users\KAA
> FLB\Documents\R\win-library\2.15\rJava\jri\x64
>
> Please let us know how you get on.
>
> Regards,
> Chris.
>
> P.S. Don't forget to include
> mzmine-devel@lists.sourceforge.net<mailto:mzmine-devel@lists.sourceforge.net>
> in your responses, then the entire list can help out.
>
> On 19/12/12 10:21, Konstantinos Aliferis, Dr wrote:
>> Hi Chris,
>>
>> Thank you for your reply.
>>
>> I followed the steps carefully and now all work well, with the
>> exception of XCMS module for chromatogram deconvolution.
>>
>> Often I get the error about the JAVA(TM) Platform SE binary (please
>> see attached).
>>
>> Is it a bug? Is there any way to make it work?
>>
>> As per your request:
>>
>> .libPaths() in R gives:
>>
>> [1] "C:/Users/KAA FLB/Documents/R/win-library/2.15"
>>
>> [2] "C:/Program Files/R/R-2.15.2/library"
>>
>> And .packageDescription("ptw"):
>>
>> *********************************************************************
>> *
>> *************
>>
>> Package: ptw
>>
>> Type: Package
>>
>> Title: Parametric Time Warping
>>
>> Version: 1.0-4
>>
>> Date: 2012-07-30
>>
>> Author: Jan Gerretzen
>> <j.gerret...@science.ru.nl<mailto:j.gerret...@science.ru.nl>>, Paul Eilers
>> <p.eil...@erasmusmc.nl<mailto:p.eil...@erasmusmc.nl>>, Hans Wouters, Tom
>> Bloemberg
>> <t.bloemb...@science.ru.nl<mailto:t.bloemb...@science.ru.nl>>, Ron Wehrens
>>
>> <ron.wehr...@fmach.it<mailto:ron.wehr...@fmach.it>> and The R Development
>> Core Team
>>
>> Maintainer: Tom Bloemberg
>> <t.bloemb...@science.ru.nl<mailto:t.bloemb...@science.ru.nl>>
>>
>> Description: Parametric Time Warping aligns patterns, i.e. it aims to
>> put corresponding features at the same locations. The algorithm
>> searches for an optimal polynomial
>>
>> describing the warping. It is possible to align one sample to a
>> reference, several samples to the same reference, or several samples
>> to several
>>
>> references. One can choose between calculating individual warpings,
>> or one global warping for a set of samples and one reference. Two
>> optimization
>>
>> criteria are implemented: RMS (Root Mean Square error) and WCC
>> (Weighted Cross Correlation).
>>
>> License: GPL (>= 2)
>>
>> LazyLoad: yes
>>
>> Repository: CRAN
>>
>> Date/Publication: 2012-08-08 08:35:53
>>
>> Packaged: 2012-08-08 08:13:26 UTC; tombloem
>>
>> Built: R 2.15.2; x86_64-w64-mingw32; 2012-10-31 19:40:53 UTC; windows
>>
>> -- File: C:/Users/KAA
>> FLB/Documents/R/win-library/2.15/ptw/Meta/package.rds
>>
>> *********************************************************************
>> *
>> ***********
>>
>> Thank you again, your assistance is greatly appreciated.
>>
>> Cheers
>>
>> Kostas
>>
>> *From:*Pudney Chris (ext) GBJH [mailto:chris.pud...@syngenta.com]
>> *Sent:* December-17-12 9:45 PM
>> *To:* Konstantinos Aliferis, Dr
>> *Cc:*
>> mzmine-devel@lists.sourceforge.net<mailto:mzmine-devel@lists.sourceforge.net>
>> <mailto:mzmine-devel@lists.sourceforge.net>
>> *Subject:* Re: [Mzmine-devel] MZmine troubleshooting
>>
>> G'day,
>>
>> Kostas, firstly you need to make sure that certain packages are
>> installed in R for the CAMERA and baseline correction modules to
>> work, see the MZmine manual:
>>
>> https://docs.google.com/document/pub?id=1JtdNwp1y6wz_Boz8qVGESH-kSrMh
>> c
>> GaJWR18iGmhstU#h.1pys305nsw0o
>>
>>
>> Please start R and run the following commands:
>>
>> install.packages(c("rJava", "ptw", "gplots"))
>> source("http://bioconductor.org/biocLite.R";
>> <http://bioconductor.org/biocLite.R>)
>> biocLite("xcms")
>> biocLite("CAMERA")
>>
>> Then you need to configure your start-up script correctly. Please
>> start R and send us the output from the following commands:
>>
>> .libPaths()
>> .packageDescription("ptw")
>>
>> Regards,
>> Chris.
>>
>> -----
>>
>> Dear MZmine Developers team:
>>
>> I am running MZmine 2.10 on a PC-Windows 7, 12 Core i7, 24GB Ram.
>>
>> I am experiencing problems with the settings in the startMZmine script.
>>
>> It seems I cannot figure out how to set the paths to R for Baseline
>> corrections and CAMERA searches. R is install in this PC.
>>
>> Please find attached screenshots and the startMZmine script.
>>
>> Any help would be greatly appreciated.
>>
>> Thank you
>>
>> Kind Regards
>>
>> Kostas
>>
>>
>>
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>> --
>>
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